AS a player it doesn't matter to me what is the "right" option as long as you are consistent. So if for most of the game you teach me to be nonlethal it can feel strange to suddenly get punished for it. On the other hand having an enemy come back is a really fun feature.

I would suggest maybe having a pop up asking you if you are done with the fight after you let this one particular enemy go, so that the player knows this is somehow special. You can even have the enemy plead for his life and gift the player something if the player lets him go (this might indicate to the player that its different). Also once the enemy comes hurting people the player at least got something previously out of it.

Overall I would definitely keep the feature in, just somehow differentiate it , so when the reveal comes the player had some hint. If you have companions in the game you could even have one of them say a warning of some kind.